Multiple sequence alignment - TraesCS7B01G337900
Loading Multiple Alignment...
BLAST Results
BLAST Results - Input Sequence
Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this
to extract flanking regions for cloning. If the result of the multiple sequence alignment is
not as expected, these results could be used for further investigation.
qseqid
sseqid
percentage.identical
alignment.length
no.mismatch
no.gap.openings
qstart
qend
sstart
send
evalue
bitscore
0
TraesCS7B01G337900
chr7B
100.000
2749
0
0
1
2749
592535802
592533054
0.000000e+00
5077.0
1
TraesCS7B01G337900
chr7B
85.414
809
88
18
948
1751
592807927
592808710
0.000000e+00
813.0
2
TraesCS7B01G337900
chr7B
85.624
793
85
17
963
1751
592867734
592868501
0.000000e+00
806.0
3
TraesCS7B01G337900
chr7B
83.579
883
108
24
879
1755
592718413
592719264
0.000000e+00
793.0
4
TraesCS7B01G337900
chr7D
94.167
1423
56
16
541
1953
548916495
548915090
0.000000e+00
2143.0
5
TraesCS7B01G337900
chr7D
85.290
809
96
15
950
1755
549274330
549275118
0.000000e+00
813.0
6
TraesCS7B01G337900
chr7D
84.994
813
92
16
950
1755
549134791
549135580
0.000000e+00
798.0
7
TraesCS7B01G337900
chr7D
79.633
491
52
28
2295
2749
548914265
548913787
2.660000e-80
309.0
8
TraesCS7B01G337900
chr7D
82.712
295
15
19
1954
2225
548914944
548914663
2.130000e-56
230.0
9
TraesCS7B01G337900
chr7D
97.872
47
1
0
496
542
637671239
637671193
6.310000e-12
82.4
10
TraesCS7B01G337900
chr6B
95.795
547
17
4
1
542
129477391
129476846
0.000000e+00
878.0
11
TraesCS7B01G337900
chr7A
85.190
817
95
17
950
1760
634605500
634606296
0.000000e+00
815.0
12
TraesCS7B01G337900
chr7A
85.099
812
92
15
950
1755
634476928
634477716
0.000000e+00
802.0
13
TraesCS7B01G337900
chr7A
84.852
812
94
15
950
1755
634463998
634464786
0.000000e+00
791.0
14
TraesCS7B01G337900
chr7A
96.000
50
2
0
493
542
291021918
291021967
6.310000e-12
82.4
15
TraesCS7B01G337900
chr5A
93.738
543
30
4
1
542
547825330
547825869
0.000000e+00
811.0
16
TraesCS7B01G337900
chrUn
93.186
543
34
3
1
542
420212719
420212179
0.000000e+00
795.0
17
TraesCS7B01G337900
chrUn
93.002
543
35
3
1
542
379544268
379543728
0.000000e+00
789.0
18
TraesCS7B01G337900
chrUn
91.927
545
41
3
1
544
37054160
37053618
0.000000e+00
760.0
19
TraesCS7B01G337900
chr3A
95.254
295
14
0
1
295
738183693
738183987
4.150000e-128
468.0
20
TraesCS7B01G337900
chr2B
92.308
52
4
0
493
544
780580192
780580243
1.060000e-09
75.0
21
TraesCS7B01G337900
chr1A
93.333
45
3
0
493
537
44289338
44289382
1.770000e-07
67.6
22
TraesCS7B01G337900
chr3D
95.000
40
2
0
2105
2144
582052649
582052610
2.290000e-06
63.9
BLAST Results - HSPs grouped
These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the
BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are
purely upstream or downstream may be removed if they don't overlap both primers.
query
scaffold
start
end
length
rev.comp
avg.bitscore
max.bitscore
avg.percent.identical
query.start
query.end
num_hsp
groupid
homo_length
0
TraesCS7B01G337900
chr7B
592533054
592535802
2748
True
5077
5077
100.000
1
2749
1
chr7B.!!$R1
2748
1
TraesCS7B01G337900
chr7B
592807927
592808710
783
False
813
813
85.414
948
1751
1
chr7B.!!$F2
803
2
TraesCS7B01G337900
chr7B
592867734
592868501
767
False
806
806
85.624
963
1751
1
chr7B.!!$F3
788
3
TraesCS7B01G337900
chr7B
592718413
592719264
851
False
793
793
83.579
879
1755
1
chr7B.!!$F1
876
4
TraesCS7B01G337900
chr7D
548913787
548916495
2708
True
894
2143
85.504
541
2749
3
chr7D.!!$R2
2208
5
TraesCS7B01G337900
chr7D
549274330
549275118
788
False
813
813
85.290
950
1755
1
chr7D.!!$F2
805
6
TraesCS7B01G337900
chr7D
549134791
549135580
789
False
798
798
84.994
950
1755
1
chr7D.!!$F1
805
7
TraesCS7B01G337900
chr6B
129476846
129477391
545
True
878
878
95.795
1
542
1
chr6B.!!$R1
541
8
TraesCS7B01G337900
chr7A
634605500
634606296
796
False
815
815
85.190
950
1760
1
chr7A.!!$F4
810
9
TraesCS7B01G337900
chr7A
634476928
634477716
788
False
802
802
85.099
950
1755
1
chr7A.!!$F3
805
10
TraesCS7B01G337900
chr7A
634463998
634464786
788
False
791
791
84.852
950
1755
1
chr7A.!!$F2
805
11
TraesCS7B01G337900
chr5A
547825330
547825869
539
False
811
811
93.738
1
542
1
chr5A.!!$F1
541
12
TraesCS7B01G337900
chrUn
420212179
420212719
540
True
795
795
93.186
1
542
1
chrUn.!!$R3
541
13
TraesCS7B01G337900
chrUn
379543728
379544268
540
True
789
789
93.002
1
542
1
chrUn.!!$R2
541
14
TraesCS7B01G337900
chrUn
37053618
37054160
542
True
760
760
91.927
1
544
1
chrUn.!!$R1
543
AutoCloner calculated primer pairs
These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3),
whilst remaining within the specified product range where possible.
Forward
Primers
Reverse
Primers
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
648
660
0.038599
AGCCCATGTGCTCACAATCA
59.961
50.0
6.81
0.0
45.41
2.57
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2313
2843
0.109458
CGAGTACTAACACTGCGCCA
60.109
55.0
4.18
0.0
0.0
5.69
R
All possible primers
Listed here are all possible primers based on the multiple sequence alignment and SNPs generated
previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work
during PCR or sequencing,
these could be used as alternatives.
Forward
Primers
Reverse
Primers
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
69
70
0.887933
GCCAAACCACCTACCATGTG
59.112
55.000
0.00
0.00
0.00
3.21
157
158
2.050350
GTCGTCAGATCCCCACCGA
61.050
63.158
0.00
0.00
0.00
4.69
373
375
3.849574
TGGAGGTGGTTTGGATTATGAGA
59.150
43.478
0.00
0.00
0.00
3.27
464
470
0.179032
AACGTGGGATGTTGTCTGCA
60.179
50.000
0.00
0.00
0.00
4.41
502
510
1.691434
GATGACAGGAGATGGAGGTCC
59.309
57.143
0.00
0.00
0.00
4.46
582
590
3.763897
CCCTTTGGAATAGAACAACCCTG
59.236
47.826
0.00
0.00
0.00
4.45
584
592
2.507407
TGGAATAGAACAACCCTGCC
57.493
50.000
0.00
0.00
0.00
4.85
646
658
0.892755
CAAGCCCATGTGCTCACAAT
59.107
50.000
2.23
0.00
45.41
2.71
647
659
1.135199
CAAGCCCATGTGCTCACAATC
60.135
52.381
2.23
0.00
45.41
2.67
648
660
0.038599
AGCCCATGTGCTCACAATCA
59.961
50.000
6.81
0.00
45.41
2.57
649
661
0.171903
GCCCATGTGCTCACAATCAC
59.828
55.000
6.81
0.00
45.41
3.06
650
662
1.536940
CCCATGTGCTCACAATCACA
58.463
50.000
6.81
0.00
45.41
3.58
669
681
1.535462
CAAGTTGGTGAACCGTCATCC
59.465
52.381
0.00
0.00
39.43
3.51
673
685
0.535335
TGGTGAACCGTCATCCTAGC
59.465
55.000
0.00
0.00
39.43
3.42
778
790
1.321016
CTTCTTCACGCGCACATTTG
58.679
50.000
5.73
0.00
0.00
2.32
779
791
0.660488
TTCTTCACGCGCACATTTGT
59.340
45.000
5.73
0.00
0.00
2.83
789
801
2.161410
GCGCACATTTGTATCTGTTCCA
59.839
45.455
0.30
0.00
0.00
3.53
831
843
3.844577
ATCATCAAGCACAAGCAGAAC
57.155
42.857
0.00
0.00
45.49
3.01
838
850
0.169672
GCACAAGCAGAACATCGCAT
59.830
50.000
0.00
0.00
41.58
4.73
861
873
7.201418
GCATTGATCTGATACGATATCACACAG
60.201
40.741
3.12
6.68
0.00
3.66
862
874
5.703876
TGATCTGATACGATATCACACAGC
58.296
41.667
3.12
0.00
0.00
4.40
863
875
4.147219
TCTGATACGATATCACACAGCG
57.853
45.455
3.12
0.00
0.00
5.18
873
885
4.778415
ACACAGCGCGCCTACTCG
62.778
66.667
30.33
13.17
0.00
4.18
909
921
1.265905
GCTCCCAATAATTTACCCGCG
59.734
52.381
0.00
0.00
0.00
6.46
928
940
5.530171
CCCGCGTGATACTACCAGTATATAT
59.470
44.000
4.92
0.00
41.21
0.86
929
941
6.707608
CCCGCGTGATACTACCAGTATATATA
59.292
42.308
4.92
0.00
41.21
0.86
961
977
0.688487
TACCTTACCTGCAGCCGTTT
59.312
50.000
8.66
0.00
0.00
3.60
1080
1097
2.588439
GCCTTCGACCCTAACCCC
59.412
66.667
0.00
0.00
0.00
4.95
1147
1165
2.109609
TAAACGCCGTGCTAGTATCG
57.890
50.000
0.00
0.00
0.00
2.92
1163
1193
6.692249
GCTAGTATCGACTCTTTGGTTTCTAC
59.308
42.308
0.00
0.00
37.10
2.59
1166
1196
5.633830
ATCGACTCTTTGGTTTCTACGTA
57.366
39.130
0.00
0.00
0.00
3.57
1167
1197
4.787598
TCGACTCTTTGGTTTCTACGTAC
58.212
43.478
0.00
0.00
0.00
3.67
1169
1199
5.009010
TCGACTCTTTGGTTTCTACGTACTT
59.991
40.000
0.00
0.00
0.00
2.24
1170
1200
5.341727
CGACTCTTTGGTTTCTACGTACTTC
59.658
44.000
0.00
0.00
0.00
3.01
1171
1201
5.218139
ACTCTTTGGTTTCTACGTACTTCG
58.782
41.667
0.00
0.00
46.00
3.79
1172
1202
5.009010
ACTCTTTGGTTTCTACGTACTTCGA
59.991
40.000
0.00
0.00
42.86
3.71
1173
1203
5.830912
TCTTTGGTTTCTACGTACTTCGAA
58.169
37.500
0.00
0.00
42.86
3.71
1174
1204
6.272318
TCTTTGGTTTCTACGTACTTCGAAA
58.728
36.000
0.00
4.19
42.86
3.46
1175
1205
6.925165
TCTTTGGTTTCTACGTACTTCGAAAT
59.075
34.615
9.95
0.00
42.86
2.17
1176
1206
6.456447
TTGGTTTCTACGTACTTCGAAATG
57.544
37.500
9.95
0.00
42.86
2.32
1177
1207
5.531634
TGGTTTCTACGTACTTCGAAATGT
58.468
37.500
9.95
0.00
42.86
2.71
1182
1212
5.260900
TCTACGTACTTCGAAATGTGATCG
58.739
41.667
0.00
5.02
42.86
3.69
1188
1218
4.748892
ACTTCGAAATGTGATCGTCATCT
58.251
39.130
0.00
0.00
40.99
2.90
1195
1225
3.733443
TGTGATCGTCATCTATGGTGG
57.267
47.619
0.00
0.00
0.00
4.61
1196
1226
2.224042
TGTGATCGTCATCTATGGTGGC
60.224
50.000
0.00
0.00
0.00
5.01
1199
1229
3.831911
TGATCGTCATCTATGGTGGCATA
59.168
43.478
0.00
0.00
0.00
3.14
1699
1734
1.469940
CGTTGCTAAGTCGCTCCTCAT
60.470
52.381
0.00
0.00
0.00
2.90
1703
1738
1.342819
GCTAAGTCGCTCCTCATGGAT
59.657
52.381
0.00
0.00
42.29
3.41
1760
1795
1.396607
GGCCTTGATGCATGCATGGA
61.397
55.000
36.73
25.66
36.70
3.41
1773
1808
0.391130
GCATGGACACGCTGTTCCTA
60.391
55.000
0.00
0.00
0.00
2.94
1778
1813
1.202428
GGACACGCTGTTCCTATCTCC
60.202
57.143
0.00
0.00
0.00
3.71
1779
1814
1.751924
GACACGCTGTTCCTATCTCCT
59.248
52.381
0.00
0.00
0.00
3.69
1802
1837
0.168128
GTATTGTCTGCGGGCACAAC
59.832
55.000
0.00
0.00
35.37
3.32
1817
1852
2.285544
GCACAACAATTTGCAACCGTTC
60.286
45.455
0.00
0.00
38.68
3.95
1831
1866
4.143137
GCAACCGTTCCTTTGCAATAAATG
60.143
41.667
0.00
0.76
46.13
2.32
1904
1939
1.592400
TTCGCTCTGTACCTCCCACG
61.592
60.000
0.00
0.00
0.00
4.94
1953
1988
5.392767
TTGACTGTCACTGGTCTAGAATC
57.607
43.478
10.56
0.00
34.01
2.52
1954
1989
4.407365
TGACTGTCACTGGTCTAGAATCA
58.593
43.478
6.36
0.00
34.01
2.57
1955
1990
4.832823
TGACTGTCACTGGTCTAGAATCAA
59.167
41.667
6.36
0.00
34.01
2.57
1956
1991
5.047731
TGACTGTCACTGGTCTAGAATCAAG
60.048
44.000
6.36
0.00
34.01
3.02
1957
1992
5.080337
ACTGTCACTGGTCTAGAATCAAGA
58.920
41.667
0.00
0.00
0.00
3.02
1958
1993
5.184864
ACTGTCACTGGTCTAGAATCAAGAG
59.815
44.000
0.00
0.00
0.00
2.85
1959
1994
5.080337
TGTCACTGGTCTAGAATCAAGAGT
58.920
41.667
0.00
0.00
0.00
3.24
2003
2182
1.346068
GGCTATCCATTCCTCGAGCTT
59.654
52.381
6.99
0.00
0.00
3.74
2006
2185
4.503296
GGCTATCCATTCCTCGAGCTTTAA
60.503
45.833
6.99
0.00
0.00
1.52
2012
2191
4.095036
CCATTCCTCGAGCTTTAAACCTTC
59.905
45.833
6.99
0.00
0.00
3.46
2015
2194
3.833070
TCCTCGAGCTTTAAACCTTCTCT
59.167
43.478
6.99
0.00
0.00
3.10
2019
2198
3.611970
GAGCTTTAAACCTTCTCTCCCC
58.388
50.000
0.00
0.00
0.00
4.81
2056
2235
1.959508
GCTGCTTCCTCTCCTCTCTGA
60.960
57.143
0.00
0.00
0.00
3.27
2065
2244
3.432588
CCTCTCTGACGGTCGCGT
61.433
66.667
5.77
0.00
0.00
6.01
2146
2348
3.716006
CGCAAGCTGGTGACCACG
61.716
66.667
0.00
0.00
0.00
4.94
2147
2349
2.280797
GCAAGCTGGTGACCACGA
60.281
61.111
0.00
0.00
0.00
4.35
2148
2350
2.320587
GCAAGCTGGTGACCACGAG
61.321
63.158
0.00
7.65
39.70
4.18
2149
2351
1.069765
CAAGCTGGTGACCACGAGT
59.930
57.895
0.00
0.00
39.05
4.18
2150
2352
0.946221
CAAGCTGGTGACCACGAGTC
60.946
60.000
0.00
0.00
46.51
3.36
2151
2353
2.048127
GCTGGTGACCACGAGTCC
60.048
66.667
0.00
0.00
45.68
3.85
2152
2354
2.867855
GCTGGTGACCACGAGTCCA
61.868
63.158
0.00
0.70
45.68
4.02
2153
2355
1.006102
CTGGTGACCACGAGTCCAC
60.006
63.158
0.00
0.00
45.68
4.02
2154
2356
2.049433
GGTGACCACGAGTCCACG
60.049
66.667
0.00
0.00
45.68
4.94
2167
2369
1.450134
TCCACGACCTGCATGCATC
60.450
57.895
22.97
16.00
0.00
3.91
2168
2370
1.746239
CCACGACCTGCATGCATCA
60.746
57.895
22.97
0.00
0.00
3.07
2169
2371
1.712018
CCACGACCTGCATGCATCAG
61.712
60.000
22.97
15.40
0.00
2.90
2198
2400
2.352225
GGATCGATTCTCTCCGTGATGG
60.352
54.545
0.00
0.00
40.09
3.51
2225
2427
1.143684
ACGATGGGAGGAATCCAATGG
59.856
52.381
0.61
0.00
37.87
3.16
2226
2428
1.421268
CGATGGGAGGAATCCAATGGA
59.579
52.381
3.67
3.67
37.87
3.41
2227
2429
2.551721
CGATGGGAGGAATCCAATGGAG
60.552
54.545
8.40
0.00
37.87
3.86
2228
2430
1.985622
TGGGAGGAATCCAATGGAGT
58.014
50.000
8.40
4.62
34.05
3.85
2229
2431
1.565759
TGGGAGGAATCCAATGGAGTG
59.434
52.381
7.08
0.00
34.05
3.51
2230
2432
1.685148
GGAGGAATCCAATGGAGTGC
58.315
55.000
13.33
13.33
38.37
4.40
2232
2434
2.725221
AGGAATCCAATGGAGTGCTC
57.275
50.000
17.82
6.44
44.56
4.26
2233
2435
2.203584
AGGAATCCAATGGAGTGCTCT
58.796
47.619
17.82
4.66
44.56
4.09
2234
2436
2.172293
AGGAATCCAATGGAGTGCTCTC
59.828
50.000
17.82
7.26
44.56
3.20
2235
2437
2.172293
GGAATCCAATGGAGTGCTCTCT
59.828
50.000
13.90
0.00
35.36
3.10
2236
2438
3.465871
GAATCCAATGGAGTGCTCTCTC
58.534
50.000
7.08
6.54
40.29
3.20
2239
2441
1.134461
CCAATGGAGTGCTCTCTCAGG
60.134
57.143
14.98
8.68
40.29
3.86
2240
2442
1.134461
CAATGGAGTGCTCTCTCAGGG
60.134
57.143
14.98
5.15
40.29
4.45
2241
2443
1.336632
ATGGAGTGCTCTCTCAGGGC
61.337
60.000
14.98
0.00
40.29
5.19
2243
2445
0.396417
GGAGTGCTCTCTCAGGGCTA
60.396
60.000
14.98
0.00
40.29
3.93
2246
2448
0.179086
GTGCTCTCTCAGGGCTAAGC
60.179
60.000
0.00
0.00
0.00
3.09
2263
2757
5.224135
GCTAAGCCTGCTAGTAGATGTTAC
58.776
45.833
9.72
0.00
0.00
2.50
2287
2781
1.956477
GTTGCATGGTTGGACTCTTGT
59.044
47.619
0.00
0.00
0.00
3.16
2292
2786
3.415212
CATGGTTGGACTCTTGTGATGT
58.585
45.455
0.00
0.00
0.00
3.06
2293
2787
3.576078
TGGTTGGACTCTTGTGATGTT
57.424
42.857
0.00
0.00
0.00
2.71
2311
2841
2.168313
TGTTAGCTTGATGATCGAGGCA
59.832
45.455
11.48
0.00
0.00
4.75
2312
2842
2.799412
GTTAGCTTGATGATCGAGGCAG
59.201
50.000
11.48
0.00
0.00
4.85
2313
2843
0.829333
AGCTTGATGATCGAGGCAGT
59.171
50.000
11.48
0.00
0.00
4.40
2315
2845
1.579698
CTTGATGATCGAGGCAGTGG
58.420
55.000
1.54
0.00
0.00
4.00
2316
2846
0.462581
TTGATGATCGAGGCAGTGGC
60.463
55.000
9.02
9.02
40.13
5.01
2318
2848
4.819761
TGATCGAGGCAGTGGCGC
62.820
66.667
11.51
11.00
42.47
6.53
2323
2853
4.996434
GAGGCAGTGGCGCAGTGT
62.996
66.667
15.57
0.00
42.47
3.55
2324
2854
4.569180
AGGCAGTGGCGCAGTGTT
62.569
61.111
10.83
0.00
42.47
3.32
2325
2855
2.668212
GGCAGTGGCGCAGTGTTA
60.668
61.111
10.83
0.00
42.47
2.41
2326
2856
2.680913
GGCAGTGGCGCAGTGTTAG
61.681
63.158
10.83
0.00
42.47
2.34
2327
2857
1.961277
GCAGTGGCGCAGTGTTAGT
60.961
57.895
10.83
0.00
37.16
2.24
2328
2858
0.669318
GCAGTGGCGCAGTGTTAGTA
60.669
55.000
10.83
0.00
37.16
1.82
2329
2859
1.068474
CAGTGGCGCAGTGTTAGTAC
58.932
55.000
10.83
0.00
30.89
2.73
2330
2860
0.966920
AGTGGCGCAGTGTTAGTACT
59.033
50.000
10.83
0.00
0.00
2.73
2331
2861
1.067776
AGTGGCGCAGTGTTAGTACTC
60.068
52.381
10.83
0.00
0.00
2.59
2334
2864
1.202268
GGCGCAGTGTTAGTACTCGAT
60.202
52.381
10.83
0.00
0.00
3.59
2337
2867
2.846550
CGCAGTGTTAGTACTCGATGTG
59.153
50.000
0.00
0.00
0.00
3.21
2338
2868
3.179830
GCAGTGTTAGTACTCGATGTGG
58.820
50.000
0.00
0.00
0.00
4.17
2339
2869
3.367087
GCAGTGTTAGTACTCGATGTGGT
60.367
47.826
0.00
0.00
0.00
4.16
2340
2870
4.142534
GCAGTGTTAGTACTCGATGTGGTA
60.143
45.833
0.00
0.00
0.00
3.25
2341
2871
5.570344
CAGTGTTAGTACTCGATGTGGTAG
58.430
45.833
0.00
0.00
0.00
3.18
2342
2872
5.353400
CAGTGTTAGTACTCGATGTGGTAGA
59.647
44.000
0.00
0.00
0.00
2.59
2351
2881
1.405526
CGATGTGGTAGAGTTGGTGGG
60.406
57.143
0.00
0.00
0.00
4.61
2352
2882
1.906574
GATGTGGTAGAGTTGGTGGGA
59.093
52.381
0.00
0.00
0.00
4.37
2354
2884
0.613777
GTGGTAGAGTTGGTGGGAGG
59.386
60.000
0.00
0.00
0.00
4.30
2355
2885
0.490017
TGGTAGAGTTGGTGGGAGGA
59.510
55.000
0.00
0.00
0.00
3.71
2357
2887
1.486726
GGTAGAGTTGGTGGGAGGATG
59.513
57.143
0.00
0.00
0.00
3.51
2359
2889
2.277008
AGAGTTGGTGGGAGGATGAT
57.723
50.000
0.00
0.00
0.00
2.45
2373
2903
1.134818
GGATGATATGTATCGCCCGCA
60.135
52.381
0.00
0.00
35.48
5.69
2374
2904
2.196749
GATGATATGTATCGCCCGCAG
58.803
52.381
0.00
0.00
35.48
5.18
2375
2905
0.389817
TGATATGTATCGCCCGCAGC
60.390
55.000
0.00
0.00
35.48
5.25
2384
2914
3.127533
GCCCGCAGCGTTCTTGAT
61.128
61.111
15.05
0.00
0.00
2.57
2386
2916
1.741401
CCCGCAGCGTTCTTGATCA
60.741
57.895
15.05
0.00
0.00
2.92
2426
2960
3.760035
CCGGCTAGCGTGGAGTGT
61.760
66.667
17.37
0.00
0.00
3.55
2440
2974
1.668419
GAGTGTGCCGGCAGAATATT
58.332
50.000
33.73
15.20
0.00
1.28
2444
2978
1.295792
GTGCCGGCAGAATATTTCGA
58.704
50.000
33.73
0.00
34.02
3.71
2447
2981
2.290367
TGCCGGCAGAATATTTCGAATG
59.710
45.455
29.03
0.00
34.02
2.67
2454
2988
5.106908
GGCAGAATATTTCGAATGGCTAGAC
60.107
44.000
12.04
0.00
34.02
2.59
2455
2989
5.466728
GCAGAATATTTCGAATGGCTAGACA
59.533
40.000
0.00
0.00
34.02
3.41
2456
2990
6.347240
GCAGAATATTTCGAATGGCTAGACAG
60.347
42.308
3.72
0.00
34.02
3.51
2465
2999
4.335874
CGAATGGCTAGACAGTACTACAGT
59.664
45.833
3.72
0.00
0.00
3.55
2469
3003
3.565063
GGCTAGACAGTACTACAGTAGCC
59.435
52.174
20.49
20.49
33.98
3.93
2478
3012
5.236047
CAGTACTACAGTAGCCTAGTTACGG
59.764
48.000
7.57
0.00
0.00
4.02
2481
3015
5.012893
ACTACAGTAGCCTAGTTACGGTTT
58.987
41.667
7.57
0.71
31.72
3.27
2489
3023
3.316029
GCCTAGTTACGGTTTGTGGTTTT
59.684
43.478
0.00
0.00
0.00
2.43
2501
3035
6.073494
CGGTTTGTGGTTTTTCTTTCTGTTTT
60.073
34.615
0.00
0.00
0.00
2.43
2532
3073
7.835634
TTAATTTTCCACTTCACCACAAAAC
57.164
32.000
0.00
0.00
0.00
2.43
2535
3076
2.096248
TCCACTTCACCACAAAACACC
58.904
47.619
0.00
0.00
0.00
4.16
2555
3096
7.206981
ACACCTTTCATACAACAATTGAGAG
57.793
36.000
13.59
3.78
0.00
3.20
2558
3099
7.805071
CACCTTTCATACAACAATTGAGAGTTC
59.195
37.037
13.59
0.00
0.00
3.01
2559
3100
7.502226
ACCTTTCATACAACAATTGAGAGTTCA
59.498
33.333
13.59
0.00
0.00
3.18
2561
3102
9.734620
CTTTCATACAACAATTGAGAGTTCAAA
57.265
29.630
13.59
3.05
45.82
2.69
2746
3310
8.891720
AGTAACACAATGAACAATTTGCAATTT
58.108
25.926
0.00
0.00
0.00
1.82
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
157
158
1.342819
GGAGCGAGGACATGCTTAGAT
59.657
52.381
0.00
0.00
42.60
1.98
295
296
2.283894
TCGGCTCCTGCTTCCTCA
60.284
61.111
0.00
0.00
39.59
3.86
341
343
0.325671
ACCACCTCCATGTCGATCCT
60.326
55.000
0.00
0.00
0.00
3.24
373
375
3.492353
CTCCCACGCCCCCATCAT
61.492
66.667
0.00
0.00
0.00
2.45
502
510
3.186409
AGAATTGAACGTCGTGATGGTTG
59.814
43.478
0.00
0.00
0.00
3.77
582
590
0.895100
TGGGAGCAGTTGATTGTGGC
60.895
55.000
0.00
0.00
0.00
5.01
584
592
1.538512
CAGTGGGAGCAGTTGATTGTG
59.461
52.381
0.00
0.00
0.00
3.33
646
658
1.066071
TGACGGTTCACCAACTTGTGA
60.066
47.619
0.00
0.00
43.26
3.58
647
659
1.374560
TGACGGTTCACCAACTTGTG
58.625
50.000
0.00
0.00
37.59
3.33
648
660
2.218603
GATGACGGTTCACCAACTTGT
58.781
47.619
0.00
0.00
33.38
3.16
649
661
1.535462
GGATGACGGTTCACCAACTTG
59.465
52.381
0.00
0.00
33.38
3.16
650
662
1.420138
AGGATGACGGTTCACCAACTT
59.580
47.619
0.00
0.00
33.38
2.66
661
673
3.616721
CGGGGGCTAGGATGACGG
61.617
72.222
0.00
0.00
0.00
4.79
740
752
3.576078
AGGATTCGATGCAACCCATTA
57.424
42.857
0.00
0.00
33.29
1.90
831
843
6.694411
TGATATCGTATCAGATCAATGCGATG
59.306
38.462
28.00
6.87
46.59
3.84
838
850
6.152379
GCTGTGTGATATCGTATCAGATCAA
58.848
40.000
15.89
0.00
30.43
2.57
861
873
2.938539
ATGAGTTCGAGTAGGCGCGC
62.939
60.000
25.94
25.94
37.81
6.86
862
874
0.525668
AATGAGTTCGAGTAGGCGCG
60.526
55.000
0.00
0.00
39.25
6.86
863
875
1.201343
GAATGAGTTCGAGTAGGCGC
58.799
55.000
0.00
0.00
0.00
6.53
873
885
2.098770
GGGAGCTTGCATGAATGAGTTC
59.901
50.000
3.33
0.00
34.85
3.01
928
940
7.293299
TGCAGGTAAGGTAGGAGTAGTAGTATA
59.707
40.741
0.00
0.00
0.00
1.47
929
941
6.102321
TGCAGGTAAGGTAGGAGTAGTAGTAT
59.898
42.308
0.00
0.00
0.00
2.12
941
953
0.249398
AACGGCTGCAGGTAAGGTAG
59.751
55.000
17.12
0.00
0.00
3.18
947
959
1.192146
AGGAGAAACGGCTGCAGGTA
61.192
55.000
17.12
0.00
0.00
3.08
1080
1097
1.216710
GACGCAGAAGTCCTGGAGG
59.783
63.158
0.00
0.00
43.13
4.30
1147
1165
5.341727
CGAAGTACGTAGAAACCAAAGAGTC
59.658
44.000
0.00
0.00
37.22
3.36
1163
1193
3.849708
TGACGATCACATTTCGAAGTACG
59.150
43.478
0.00
4.16
39.81
3.67
1166
1196
4.748892
AGATGACGATCACATTTCGAAGT
58.251
39.130
0.00
0.00
39.81
3.01
1167
1197
6.128982
CCATAGATGACGATCACATTTCGAAG
60.129
42.308
0.00
0.00
39.81
3.79
1169
1199
5.221244
ACCATAGATGACGATCACATTTCGA
60.221
40.000
0.00
0.00
39.81
3.71
1170
1200
4.984785
ACCATAGATGACGATCACATTTCG
59.015
41.667
0.00
0.00
42.20
3.46
1171
1201
5.178252
CCACCATAGATGACGATCACATTTC
59.822
44.000
0.00
0.00
0.00
2.17
1172
1202
5.059161
CCACCATAGATGACGATCACATTT
58.941
41.667
0.00
2.18
0.00
2.32
1173
1203
4.635223
CCACCATAGATGACGATCACATT
58.365
43.478
0.00
0.00
0.00
2.71
1174
1204
3.555795
GCCACCATAGATGACGATCACAT
60.556
47.826
0.00
2.63
0.00
3.21
1175
1205
2.224042
GCCACCATAGATGACGATCACA
60.224
50.000
0.00
0.00
0.00
3.58
1176
1206
2.224042
TGCCACCATAGATGACGATCAC
60.224
50.000
0.00
0.00
0.00
3.06
1177
1207
2.038659
TGCCACCATAGATGACGATCA
58.961
47.619
0.00
0.00
0.00
2.92
1182
1212
2.069273
GCGTATGCCACCATAGATGAC
58.931
52.381
0.00
0.00
34.72
3.06
1188
1218
1.885388
GCACGCGTATGCCACCATA
60.885
57.895
13.44
0.00
39.86
2.74
1314
1349
3.751246
CGCCGAGAACCCGTACCA
61.751
66.667
0.00
0.00
0.00
3.25
1547
1582
4.335647
AAGTGCACGAGCCCCTGG
62.336
66.667
12.01
0.00
41.13
4.45
1595
1630
1.365633
GCTGAGGGAGGCGTAGATG
59.634
63.158
0.00
0.00
0.00
2.90
1682
1717
0.461548
CCATGAGGAGCGACTTAGCA
59.538
55.000
0.00
0.00
40.15
3.49
1699
1734
2.717044
CCGACGGTGTGCCTATCCA
61.717
63.158
5.48
0.00
0.00
3.41
1703
1738
3.066190
CTCCCGACGGTGTGCCTA
61.066
66.667
13.94
0.00
0.00
3.93
1760
1795
1.751924
GAGGAGATAGGAACAGCGTGT
59.248
52.381
0.00
0.00
0.00
4.49
1773
1808
2.363680
CGCAGACAATACAGGAGGAGAT
59.636
50.000
0.00
0.00
0.00
2.75
1778
1813
0.811616
GCCCGCAGACAATACAGGAG
60.812
60.000
0.00
0.00
0.00
3.69
1779
1814
1.220749
GCCCGCAGACAATACAGGA
59.779
57.895
0.00
0.00
0.00
3.86
1802
1837
3.857923
CAAAGGAACGGTTGCAAATTG
57.142
42.857
14.88
11.84
0.00
2.32
1817
1852
5.005012
CGCAGATGTTCATTTATTGCAAAGG
59.995
40.000
1.71
0.00
0.00
3.11
1831
1866
1.267732
CGAAATCCAGCGCAGATGTTC
60.268
52.381
11.47
15.02
45.74
3.18
1904
1939
4.750460
TCACAAGGAGACACACGC
57.250
55.556
0.00
0.00
0.00
5.34
1953
1988
5.920273
GTCTCTCTTCAGTCTTGAACTCTTG
59.080
44.000
0.00
0.00
38.37
3.02
1954
1989
5.278266
CGTCTCTCTTCAGTCTTGAACTCTT
60.278
44.000
0.00
0.00
38.37
2.85
1955
1990
4.215399
CGTCTCTCTTCAGTCTTGAACTCT
59.785
45.833
0.00
0.00
38.37
3.24
1956
1991
4.472286
CGTCTCTCTTCAGTCTTGAACTC
58.528
47.826
0.00
0.00
38.37
3.01
1957
1992
3.254657
CCGTCTCTCTTCAGTCTTGAACT
59.745
47.826
0.00
0.00
38.37
3.01
1958
1993
3.253677
TCCGTCTCTCTTCAGTCTTGAAC
59.746
47.826
0.00
0.00
38.37
3.18
1959
1994
3.253677
GTCCGTCTCTCTTCAGTCTTGAA
59.746
47.826
0.00
0.00
40.92
2.69
2003
2182
0.616891
GCCGGGGAGAGAAGGTTTAA
59.383
55.000
2.18
0.00
0.00
1.52
2006
2185
3.009714
GGCCGGGGAGAGAAGGTT
61.010
66.667
2.18
0.00
0.00
3.50
2012
2191
3.470888
ATTGACGGCCGGGGAGAG
61.471
66.667
31.76
0.00
0.00
3.20
2015
2194
4.402528
CACATTGACGGCCGGGGA
62.403
66.667
31.76
14.83
0.00
4.81
2065
2244
1.019805
TGCAACGTTTGTGTCCACGA
61.020
50.000
0.00
0.00
39.76
4.35
2142
2344
2.258591
CAGGTCGTGGACTCGTGG
59.741
66.667
0.00
0.00
32.47
4.94
2146
2348
2.103042
GCATGCAGGTCGTGGACTC
61.103
63.158
14.21
0.00
32.47
3.36
2147
2349
2.046892
GCATGCAGGTCGTGGACT
60.047
61.111
14.21
0.00
32.47
3.85
2148
2350
1.709147
GATGCATGCAGGTCGTGGAC
61.709
60.000
26.69
4.96
34.79
4.02
2149
2351
1.450134
GATGCATGCAGGTCGTGGA
60.450
57.895
26.69
0.00
36.45
4.02
2150
2352
1.712018
CTGATGCATGCAGGTCGTGG
61.712
60.000
26.69
9.82
32.31
4.94
2151
2353
1.719709
CTGATGCATGCAGGTCGTG
59.280
57.895
26.69
12.16
34.80
4.35
2152
2354
2.110967
GCTGATGCATGCAGGTCGT
61.111
57.895
26.69
8.70
39.41
4.34
2153
2355
2.110352
TGCTGATGCATGCAGGTCG
61.110
57.895
26.69
15.47
45.31
4.79
2154
2356
3.914094
TGCTGATGCATGCAGGTC
58.086
55.556
26.69
19.50
45.31
3.85
2167
2369
1.617850
AGAATCGATCCCTAGCTGCTG
59.382
52.381
13.43
2.21
0.00
4.41
2168
2370
1.892474
GAGAATCGATCCCTAGCTGCT
59.108
52.381
7.57
7.57
0.00
4.24
2169
2371
1.892474
AGAGAATCGATCCCTAGCTGC
59.108
52.381
0.00
0.00
42.67
5.25
2178
2380
2.554462
TCCATCACGGAGAGAATCGATC
59.446
50.000
0.00
0.00
39.64
3.69
2198
2400
3.594134
GATTCCTCCCATCGTGATCATC
58.406
50.000
0.00
0.00
0.00
2.92
2209
2411
1.565759
CACTCCATTGGATTCCTCCCA
59.434
52.381
5.70
0.00
41.29
4.37
2225
2427
1.408702
CTTAGCCCTGAGAGAGCACTC
59.591
57.143
2.51
2.51
42.90
3.51
2226
2428
1.484038
CTTAGCCCTGAGAGAGCACT
58.516
55.000
0.00
0.00
0.00
4.40
2227
2429
0.179086
GCTTAGCCCTGAGAGAGCAC
60.179
60.000
0.00
0.00
0.00
4.40
2228
2430
1.333636
GGCTTAGCCCTGAGAGAGCA
61.334
60.000
13.12
0.00
44.06
4.26
2229
2431
1.445518
GGCTTAGCCCTGAGAGAGC
59.554
63.158
13.12
0.00
44.06
4.09
2240
2442
4.329462
AACATCTACTAGCAGGCTTAGC
57.671
45.455
0.00
0.00
0.00
3.09
2241
2443
5.536916
AGGTAACATCTACTAGCAGGCTTAG
59.463
44.000
0.00
0.00
41.41
2.18
2243
2445
4.290942
AGGTAACATCTACTAGCAGGCTT
58.709
43.478
0.00
0.00
41.41
4.35
2246
2448
5.599999
ACAAGGTAACATCTACTAGCAGG
57.400
43.478
0.00
0.00
41.41
4.85
2247
2449
5.292101
GCAACAAGGTAACATCTACTAGCAG
59.708
44.000
0.00
0.00
41.41
4.24
2248
2450
5.175859
GCAACAAGGTAACATCTACTAGCA
58.824
41.667
0.00
0.00
41.41
3.49
2249
2451
5.175859
TGCAACAAGGTAACATCTACTAGC
58.824
41.667
0.00
0.00
41.41
3.42
2250
2452
6.258727
CCATGCAACAAGGTAACATCTACTAG
59.741
42.308
0.00
0.00
41.41
2.57
2251
2453
6.112734
CCATGCAACAAGGTAACATCTACTA
58.887
40.000
0.00
0.00
41.41
1.82
2252
2454
4.943705
CCATGCAACAAGGTAACATCTACT
59.056
41.667
0.00
0.00
41.41
2.57
2253
2455
4.700213
ACCATGCAACAAGGTAACATCTAC
59.300
41.667
0.00
0.00
33.45
2.59
2254
2456
4.917385
ACCATGCAACAAGGTAACATCTA
58.083
39.130
0.00
0.00
33.45
1.98
2256
2458
4.236935
CAACCATGCAACAAGGTAACATC
58.763
43.478
0.00
0.00
34.15
3.06
2257
2459
3.006752
CCAACCATGCAACAAGGTAACAT
59.993
43.478
0.00
0.00
34.15
2.71
2258
2460
2.363680
CCAACCATGCAACAAGGTAACA
59.636
45.455
0.00
0.00
34.15
2.41
2263
2757
1.270550
GAGTCCAACCATGCAACAAGG
59.729
52.381
0.00
0.00
0.00
3.61
2287
2781
4.625028
CCTCGATCATCAAGCTAACATCA
58.375
43.478
0.00
0.00
0.00
3.07
2292
2786
2.432146
ACTGCCTCGATCATCAAGCTAA
59.568
45.455
0.00
0.00
0.00
3.09
2293
2787
2.034878
ACTGCCTCGATCATCAAGCTA
58.965
47.619
0.00
0.00
0.00
3.32
2311
2841
0.966920
AGTACTAACACTGCGCCACT
59.033
50.000
4.18
0.00
0.00
4.00
2312
2842
1.347320
GAGTACTAACACTGCGCCAC
58.653
55.000
4.18
0.00
0.00
5.01
2313
2843
0.109458
CGAGTACTAACACTGCGCCA
60.109
55.000
4.18
0.00
0.00
5.69
2315
2845
1.846782
CATCGAGTACTAACACTGCGC
59.153
52.381
0.00
0.00
0.00
6.09
2316
2846
2.846550
CACATCGAGTACTAACACTGCG
59.153
50.000
0.00
0.00
0.00
5.18
2318
2848
4.436242
ACCACATCGAGTACTAACACTG
57.564
45.455
0.00
0.00
0.00
3.66
2323
2853
5.356190
CCAACTCTACCACATCGAGTACTAA
59.644
44.000
0.00
0.00
37.04
2.24
2324
2854
4.880120
CCAACTCTACCACATCGAGTACTA
59.120
45.833
0.00
0.00
37.04
1.82
2325
2855
3.695060
CCAACTCTACCACATCGAGTACT
59.305
47.826
0.00
0.00
37.04
2.73
2326
2856
3.442977
ACCAACTCTACCACATCGAGTAC
59.557
47.826
0.00
0.00
37.04
2.73
2327
2857
3.442625
CACCAACTCTACCACATCGAGTA
59.557
47.826
0.00
0.00
37.04
2.59
2328
2858
2.231478
CACCAACTCTACCACATCGAGT
59.769
50.000
0.00
0.00
39.53
4.18
2329
2859
2.417379
CCACCAACTCTACCACATCGAG
60.417
54.545
0.00
0.00
0.00
4.04
2330
2860
1.548719
CCACCAACTCTACCACATCGA
59.451
52.381
0.00
0.00
0.00
3.59
2331
2861
1.405526
CCCACCAACTCTACCACATCG
60.406
57.143
0.00
0.00
0.00
3.84
2334
2864
1.348064
CTCCCACCAACTCTACCACA
58.652
55.000
0.00
0.00
0.00
4.17
2337
2867
1.486726
CATCCTCCCACCAACTCTACC
59.513
57.143
0.00
0.00
0.00
3.18
2338
2868
2.467880
TCATCCTCCCACCAACTCTAC
58.532
52.381
0.00
0.00
0.00
2.59
2339
2869
2.940514
TCATCCTCCCACCAACTCTA
57.059
50.000
0.00
0.00
0.00
2.43
2340
2870
2.277008
ATCATCCTCCCACCAACTCT
57.723
50.000
0.00
0.00
0.00
3.24
2341
2871
3.392616
ACATATCATCCTCCCACCAACTC
59.607
47.826
0.00
0.00
0.00
3.01
2342
2872
3.397527
ACATATCATCCTCCCACCAACT
58.602
45.455
0.00
0.00
0.00
3.16
2351
2881
2.799917
GCGGGCGATACATATCATCCTC
60.800
54.545
0.00
0.00
32.98
3.71
2352
2882
1.137086
GCGGGCGATACATATCATCCT
59.863
52.381
0.00
0.00
32.98
3.24
2354
2884
2.196749
CTGCGGGCGATACATATCATC
58.803
52.381
0.00
0.00
32.98
2.92
2355
2885
1.740380
GCTGCGGGCGATACATATCAT
60.740
52.381
0.00
0.00
32.98
2.45
2357
2887
2.373938
GCTGCGGGCGATACATATC
58.626
57.895
0.00
0.00
0.00
1.63
2373
2903
1.929836
GATCGCTTGATCAAGAACGCT
59.070
47.619
34.43
21.72
46.42
5.07
2374
2904
2.359523
GATCGCTTGATCAAGAACGC
57.640
50.000
34.43
20.75
46.42
4.84
2426
2960
2.031258
TTCGAAATATTCTGCCGGCA
57.969
45.000
30.59
30.59
0.00
5.69
2440
2974
4.945543
TGTAGTACTGTCTAGCCATTCGAA
59.054
41.667
5.39
0.00
0.00
3.71
2444
2978
5.299782
GCTACTGTAGTACTGTCTAGCCATT
59.700
44.000
15.27
0.00
30.33
3.16
2447
2981
3.565063
GGCTACTGTAGTACTGTCTAGCC
59.435
52.174
25.86
25.86
41.36
3.93
2454
2988
5.236047
CCGTAACTAGGCTACTGTAGTACTG
59.764
48.000
15.71
5.69
0.00
2.74
2455
2989
5.104735
ACCGTAACTAGGCTACTGTAGTACT
60.105
44.000
15.71
15.36
0.00
2.73
2456
2990
5.119694
ACCGTAACTAGGCTACTGTAGTAC
58.880
45.833
15.71
9.53
0.00
2.73
2465
2999
2.899256
ACCACAAACCGTAACTAGGCTA
59.101
45.455
0.00
0.00
0.00
3.93
2469
3003
6.367686
AGAAAAACCACAAACCGTAACTAG
57.632
37.500
0.00
0.00
0.00
2.57
2521
3055
4.950475
TGTATGAAAGGTGTTTTGTGGTGA
59.050
37.500
0.00
0.00
0.00
4.02
2522
3056
5.255710
TGTATGAAAGGTGTTTTGTGGTG
57.744
39.130
0.00
0.00
0.00
4.17
2527
3061
8.417780
TCAATTGTTGTATGAAAGGTGTTTTG
57.582
30.769
5.13
0.00
0.00
2.44
2532
3073
7.206981
ACTCTCAATTGTTGTATGAAAGGTG
57.793
36.000
5.13
0.00
0.00
4.00
2535
3076
9.734620
TTTGAACTCTCAATTGTTGTATGAAAG
57.265
29.630
5.13
0.00
41.22
2.62
2721
3285
8.945930
CAAATTGCAAATTGTTCATTGTGTTAC
58.054
29.630
17.40
0.00
0.00
2.50
2723
3287
6.472808
GCAAATTGCAAATTGTTCATTGTGTT
59.527
30.769
24.27
0.00
44.26
3.32
2725
3289
6.427300
GCAAATTGCAAATTGTTCATTGTG
57.573
33.333
24.27
3.28
44.26
3.33
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.